Mercurial > repos > devteam > emboss_5
annotate emboss_prettyplot.xml @ 18:63dd26468588 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"
author | iuc |
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date | Fri, 09 Jul 2021 18:36:34 +0000 |
parents | 8992d258e42f |
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rev | line source |
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8992d258e42f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
iuc
parents:
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1 <tool id="EMBOSS: prettyplot79" name="prettyplot" version="@VERSION@.1"> |
10
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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2 <!-- produces png output with file name --> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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3 <description>Displays aligned sequences, with colouring and boxing</description> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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4 <macros> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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5 <import>macros.xml</import> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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6 </macros> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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7 <expand macro="requirements" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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8 <command>prettyplot -sequences '$input1' -graph png -goutfile '$out_file1' -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity '$cidentity' -csimilarity '$csimilarity' |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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9 -cother '$cother' -docolour $docolour -gtitle $title -pair '$pair' -identity $identity -box $box -boxcol $boxcol -boxcolval '$boxcolval' -name $name -maxnamelen $maxnamelen -number $number -listoptions |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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10 $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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11 <inputs> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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12 <param name="input1" type="data" format="data" label="Sequence" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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13 <param name="residuesperline" type="integer" value="50" label="The number of residues to be displayed on each line" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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14 <param name="resbreak" type="integer" value="50" label="Residues before a space" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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15 <param name="ccolours" type="select" label="Colour residues by their consensus value"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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16 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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17 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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18 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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19 <param name="cidentity" type="text" value="RED" label="Colour to display identical residues" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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20 <param name="csimilarity" type="text" value="GREEN" label="Colour to display similar residues" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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21 <param name="cother" type="text" value="BLACK" label="Colour to display other residues" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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22 <param name="docolour" type="select" label="Colour residues by table oily, amide etc."> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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23 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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24 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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25 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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26 <param name="title" type="select" label="Display the title"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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27 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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28 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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29 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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30 <param name="pair" type="text" value="1.5,1.0,0.5" label="Values to represent identical similar related" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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31 <param name="identity" type="integer" value="0" label="Only match those which are identical in all sequences" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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32 <param name="box" type="select" label="Display prettyboxes"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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changeset
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33 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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34 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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35 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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36 <param name="boxcol" type="select" label="Colour the background in the boxes"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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37 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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38 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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39 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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40 <param name="boxcolval" type="text" value="GREY" label="Colour to be used for background" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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41 <param name="name" type="select" label="Display the sequence names"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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42 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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43 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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44 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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45 <param name="maxnamelen" type="integer" value="10" label="Margin size for the sequence name" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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46 <param name="number" type="select" label="Display the residue number"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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47 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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48 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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49 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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50 <param name="listoptions" type="select" label="Display the date and options used"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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51 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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52 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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53 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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54 <param name="consensus" type="select" label="Display the consensus"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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55 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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56 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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57 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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58 <param name="collision" type="select" label="Allow collisions in calculating consensus"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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59 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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changeset
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60 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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61 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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62 <param name="alternative" type="select" label="Use alternative collisions routine"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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63 <option value="0">Normal collision check</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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64 <option value="1">Checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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65 <option value="2">If another residue has a greater than or equal to matching score and these do not match then a collision has occurred</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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66 <option value="3">Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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67 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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68 <param name="showscore" type="integer" value="-1" label="Print residue scores" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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69 <param name="portrait" type="select" label="Set page to Portrait"> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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70 <option value="no">No</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
changeset
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71 <option value="yes">Yes</option> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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72 </param> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
diff
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73 </inputs> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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74 <outputs> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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75 <data name="out_file1" format="png" /> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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76 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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77 <help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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78 You can view the original documentation here_. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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79 |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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80 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/prettyplot.html |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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81 </help> |
d49956b87f7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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82 <expand macro="citations" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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83 </tool> |